The Experts below are selected from a list of 144 Experts worldwide ranked by ideXlab platform
Todd M Lowe - One of the best experts on this subject based on the ideXlab platform.
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the ucsc Archaeal Genome browser 2012 update
Nucleic Acids Research, 2012Co-Authors: Patricia P Chan, Andrew D Holmes, Andrew M Smith, Danny Tran, Todd M LoweAbstract:The UCSC Archaeal Genome Browser (http://archaea.ucsc.edu) offers a graphical web-based resource for exploration and discovery within Archaeal and other selected microbial Genomes. By bringing together existing gene annotations, gene expression data, multiple-Genome alignments, pre-computed sequence comparisons and other specialized analysis tracks, the Genome browser is a powerful aggregator of varied genomic information. The Genome browser environment maintains the current look-and-feel of the vertebrate UCSC Genome Browser, but also integrates Archaeal and bacterial-specific tracks with a few graphic display enhancements. The browser currently contains 115 Archaeal Genomes, plus 31 Genomes of viruses known to infect archaea. Some of the recently developed or enhanced tracks visualize data from published high-throughput RNA-sequencing studies, the NCBI Conserved Domain Database, sequences from pre-Genome sequencing studies, predicted gene boundaries from three different protein gene prediction algorithms, tRNAscan-SE gene predictions with RNA secondary structures and CRISPR locus predictions. We have also developed a companion resource, the Archaeal COG Browser, to provide better search and display of arCOG gene function classifications, including their phylogenetic distribution among available Archaeal Genomes.
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transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon pyrobaculum aerophilum
Journal of Bacteriology, 2009Co-Authors: Aaron E Cozen, David L Bernick, Joshua M Stuart, Katherine S Pollard, Matthew T Weirauch, Todd M LoweAbstract:Hyperthermophilic crenarchaea in the genus Pyrobaculum are notable for respiratory versatility, but relatively little is known about the genetics or regulation of crenArchaeal respiratory pathways. We measured global gene expression in Pyrobaculum aerophilum cultured with oxygen, nitrate, arsenate and ferric iron as terminal electron acceptors to identify transcriptional patterns that differentiate these pathways. We also compared Genome sequences for four closely related species with diverse respiratory characteristics (Pyrobaculum arsenaticum, Pyrobaculum calidifontis, Pyrobaculum islandicum, and Thermoproteus neutrophilus) to identify genes associated with different respiratory capabilities. Specific patterns of gene expression in P. aerophilum were associated with aerobic respiration, nitrate respiration, arsenate respiration, and anoxia. Functional predictions based on these patterns include separate cytochrome oxidases for aerobic growth and oxygen scavenging, a nitric oxide-responsive transcriptional regulator, a multicopper oxidase involved in denitrification, and an Archaeal arsenate respiratory reductase. We were unable to identify specific genes for iron respiration, but P. aerophilum exhibited repressive transcriptional responses to iron remarkably similar to those controlled by the ferric uptake regulator in bacteria. Together, these analyses present a Genome-scale view of crenArchaeal respiratory flexibility and support a large number of functional and regulatory predictions for further investigation. The complete gene expression data set can be viewed in genomic context with the Archaeal Genome Browser at archaea.ucsc.edu.
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the ucsc Archaeal Genome browser
Nucleic Acids Research, 2006Co-Authors: Kevin L Schneider, Katherine S Pollard, Robert Baertsch, Andy Pohl, Todd M LoweAbstract:As more Archaeal Genomes are sequenced, effective research and analysis tools are needed to integrate the diverse information available for any given locus. The feature-rich UCSC Genome Browser, created originally to annotate the human Genome, can be applied to any sequenced organism. We have created a UCSC Archaeal Genome Browser, available at http://archaea.ucsc.edu/, currently with 26 Archaeal Genomes. It displays G/C content, gene and operon annotation from multiple sources, sequence motifs (promoters and Shine-Dalgarno), microarray data, multi-Genome alignments and protein conservation across phylogenetic and habitat categories. We encourage submission of new experimental and bioinformatic analysis from contributors. The purpose of this tool is to aid biological discovery and facilitate greater collaboration within the Archaeal research community.
John N. Reeve - One of the best experts on this subject based on the ideXlab platform.
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shuttle vector expression in thermococcus kodakaraensis contributions of cis elements to protein synthesis in a hyperthermophilic archaeon
Applied and Environmental Microbiology, 2008Co-Authors: Thomas J Santangelo, Lubomira Cubonova, John N. ReeveAbstract:Archaea, in common with Bacteria, have small circular Genomes not encased in a nuclear compartment, with many genes organized and cotranscribed in operons. Archaeal Genome replication and expression machineries, however, have many features more similar to their eukaryotic than to their bacterial counterparts (1, 5, 9, 15). Progress in understanding Archaeal replication and gene expression has been made using purified components in vitro, but in vivo validation of the results so obtained has been limited by the lack of genetic systems. This shortcoming has been most pronounced for the thermophilic and hyperthermophilic Euryarchaea, many of which are the foci of physiological and biochemical investigations (5, 9). Fortunately progress is now being made, most notably with Thermococcus kodakaraensis (2, 8), since it was discovered that T. kodakaraensis is naturally competent for DNA uptake and incorporates donor DNA into its Genome by homologous recombination (25, 27). Deletion and mutation of chromosomal genes have resulted in the identification of novel biochemical pathways and facilitated the dissection of several events in Archaeal transcription in T. kodakaraensis (12-14, 17, 19, 22, 23, 26, 28). To overcome the need for homologous recombination, we have now constructed shuttle vectors that replicate and express genes in both T. kodakaraensis and Escherichia coli. By using plasmid expression, we have documented and quantified the roles of a ribosome binding sequence (RBS) and alternative initiation codons in Archaeal translation in T. kodakaraensis. We have also established that if one subunit (RpoL) of the multisubunit Archaeal DNA-dependent RNA polymerase (RNAP) is synthesized ectopically from a shuttle vector, it is incorporated into functional holoenzymes. Affinity tagging of this plasmid-encoded subunit has then been used to purify the 11-subunit RNAP directly from T. kodakaraensis cell lysates.
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tfe an Archaeal transcription factor in methanobacterium thermoautotrophicum related to eucaryal transcription factor tfiieα
Journal of Bacteriology, 2001Co-Authors: Brian L Hanzelka, Trevor J Darcy, John N. ReeveAbstract:In the archaeon Methanobacterium thermoautotrophicum, MTH1669 encodes a protein with a sequence related to the N-terminal sequences of the α-subunits of eucaryal general transcription factor TFIIE. The recombinant MTH1669 gene product has been purified and shown to stimulate transcription in vitro from M. thermoautotrophicum promoters that were almost inactive or much less active in reaction mixtures that contained only M. thermoautotrophicum RNA polymerase, TATA-binding protein and transcription factor B. As all complete Archaeal Genome sequences contain an MTH1669 homolog, the protein encoded by this gene is apparently the first characterized example of a transcription activator, here designated TFE, that may be universally present in the Archaea.
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archaebacteria then archaes now are there really no Archaeal pathogens
Journal of Bacteriology, 1999Co-Authors: John N. ReeveAbstract:In 1977, Carl Woese and George Fox argued that although methanogens looked like bacteria, they had very different cell wall structures and unique methanogenesis-related coenzymes and RNase T1 digestion of methanogen 16S rRNAs generated oligonucleotides so different from those from bacterial 16S rRNAs and from eukaryotic 18S rRNAs that methanogens should be placed in a third phylogenetic urkingdom, the Archaebacteria (81). They conceded that “almost nothing is known regarding their molecular biology” but concluded that “there is no reason at present to consider methanogens as any closer to eubacteria than to the cytoplasmic component of the eukaryote.” This started a scientific debate that has continued with unabated vigor for over 20 years. In 1977, methanogens were the only Archaebacteria, and not many more were predicted (81), but by 1980 the archaebacterial urkingdom had already grown to include halophiles and thermoacidophiles, and the presence of an RNA polymerase with a complex subunit configuration similar to eukaryotic RNA polymerases had been added to the list of definitive archaebacterial features (29). The 16S rRNA sequence data were by then presented in the now familiar phylogenetic tree format, and the three urkingdoms were shown arising independently from a common, less complex ancestor designated the progenote. It was tempting to comment here on the past and present arguments for and against the urkingdom concept, the number of urkingdoms, the branching relationships in the 16S rRNA phylogenetic tree, and the nature of the progenote, the universal and last common ancestors of all life (6, 9, 30, 32, 39, 49, 50, 54, 78, 81–83). But instead, from my perspective it seemed more appropriate to review how the revolutionary/heretical archaebacterial proposal has been investigated experimentally. What has been done, what were the driving forces for the research undertaken, what do we know now, what have complete Archaeal Genome sequences contributed, and what’s next?
Jorge C Escalantesemerena - One of the best experts on this subject based on the ideXlab platform.
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identification of an alternative nucleoside triphosphate 5 deoxyadenosylcobinamide phosphate nucleotidyltransferase in methanobacterium thermoautotrophicum δh
Journal of Bacteriology, 2000Co-Authors: Michael G Thomas, Jorge C EscalantesemerenaAbstract:Computer analysis of the Archaeal Genome databases failed to identify orthologues of all of the bacterial cobamide biosynthetic enzymes. Of particular interest was the lack of an orthologue of the bifunctional nucleoside triphosphate (NTP):5′-deoxyadenosylcobinamide kinase/GTP:adenosylcobinamide-phosphate guanylyltransferase enzyme (CobU in Salmonella enterica). This paper reports the identification of an Archaeal gene encoding a new nucleotidyltransferase, which is proposed to be the nonorthologous replacement of the S. enterica cobU gene. The gene encoding this nucleotidyltransferase was identified using comparative Genome analysis of the sequenced Archaeal Genomes. Orthologues of the gene encoding this activity are limited at present to members of the domain Archaea. The corresponding ORF open reading frame from Methanobacterium thermoautotrophicum ΔH (MTH1152; referred to as cobY) was amplified and cloned, and the CobY protein was expressed and purified from Escherichia coli as a hexahistidine-tagged fusion protein. This enzyme had GTP:adenosylcobinamide-phosphate guanylyltransferase activity but did not have the NTP:AdoCbi kinase activity associated with the CobU enzyme of S. enterica. NTP:adenosylcobinamide kinase activity was not detected in M. thermoautotrophicum ΔH cell extract, suggesting that this organism may not have this activity. The cobY gene complemented a cobU mutant of S. enterica grown under anaerobic conditions where growth of the cell depended on de novo adenosylcobalamin biosynthesis. cobY, however, failed to restore adenosylcobalamin biosynthesis in cobU mutants grown under aerobic conditions where de novo synthesis of this coenzyme was blocked, and growth of the cell depended on the assimilation of exogenous cobinamide. These data strongly support the proposal that the relevant cobinamide intermediates during de novo adenosylcobalamin biosynthesis are adenosylcobinamide-phosphate and adenosylcobinamide-GDP, not adenosylcobinamide. Therefore, NTP:adenosylcobinamide kinase activity is not required for de novo cobamide biosynthesis.
Michael G Thomas - One of the best experts on this subject based on the ideXlab platform.
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identification of an alternative nucleoside triphosphate 5 deoxyadenosylcobinamide phosphate nucleotidyltransferase in methanobacterium thermoautotrophicum δh
Journal of Bacteriology, 2000Co-Authors: Michael G Thomas, Jorge C EscalantesemerenaAbstract:Computer analysis of the Archaeal Genome databases failed to identify orthologues of all of the bacterial cobamide biosynthetic enzymes. Of particular interest was the lack of an orthologue of the bifunctional nucleoside triphosphate (NTP):5′-deoxyadenosylcobinamide kinase/GTP:adenosylcobinamide-phosphate guanylyltransferase enzyme (CobU in Salmonella enterica). This paper reports the identification of an Archaeal gene encoding a new nucleotidyltransferase, which is proposed to be the nonorthologous replacement of the S. enterica cobU gene. The gene encoding this nucleotidyltransferase was identified using comparative Genome analysis of the sequenced Archaeal Genomes. Orthologues of the gene encoding this activity are limited at present to members of the domain Archaea. The corresponding ORF open reading frame from Methanobacterium thermoautotrophicum ΔH (MTH1152; referred to as cobY) was amplified and cloned, and the CobY protein was expressed and purified from Escherichia coli as a hexahistidine-tagged fusion protein. This enzyme had GTP:adenosylcobinamide-phosphate guanylyltransferase activity but did not have the NTP:AdoCbi kinase activity associated with the CobU enzyme of S. enterica. NTP:adenosylcobinamide kinase activity was not detected in M. thermoautotrophicum ΔH cell extract, suggesting that this organism may not have this activity. The cobY gene complemented a cobU mutant of S. enterica grown under anaerobic conditions where growth of the cell depended on de novo adenosylcobalamin biosynthesis. cobY, however, failed to restore adenosylcobalamin biosynthesis in cobU mutants grown under aerobic conditions where de novo synthesis of this coenzyme was blocked, and growth of the cell depended on the assimilation of exogenous cobinamide. These data strongly support the proposal that the relevant cobinamide intermediates during de novo adenosylcobalamin biosynthesis are adenosylcobinamide-phosphate and adenosylcobinamide-GDP, not adenosylcobinamide. Therefore, NTP:adenosylcobinamide kinase activity is not required for de novo cobamide biosynthesis.
Katherine S Pollard - One of the best experts on this subject based on the ideXlab platform.
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transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon pyrobaculum aerophilum
Journal of Bacteriology, 2009Co-Authors: Aaron E Cozen, David L Bernick, Joshua M Stuart, Katherine S Pollard, Matthew T Weirauch, Todd M LoweAbstract:Hyperthermophilic crenarchaea in the genus Pyrobaculum are notable for respiratory versatility, but relatively little is known about the genetics or regulation of crenArchaeal respiratory pathways. We measured global gene expression in Pyrobaculum aerophilum cultured with oxygen, nitrate, arsenate and ferric iron as terminal electron acceptors to identify transcriptional patterns that differentiate these pathways. We also compared Genome sequences for four closely related species with diverse respiratory characteristics (Pyrobaculum arsenaticum, Pyrobaculum calidifontis, Pyrobaculum islandicum, and Thermoproteus neutrophilus) to identify genes associated with different respiratory capabilities. Specific patterns of gene expression in P. aerophilum were associated with aerobic respiration, nitrate respiration, arsenate respiration, and anoxia. Functional predictions based on these patterns include separate cytochrome oxidases for aerobic growth and oxygen scavenging, a nitric oxide-responsive transcriptional regulator, a multicopper oxidase involved in denitrification, and an Archaeal arsenate respiratory reductase. We were unable to identify specific genes for iron respiration, but P. aerophilum exhibited repressive transcriptional responses to iron remarkably similar to those controlled by the ferric uptake regulator in bacteria. Together, these analyses present a Genome-scale view of crenArchaeal respiratory flexibility and support a large number of functional and regulatory predictions for further investigation. The complete gene expression data set can be viewed in genomic context with the Archaeal Genome Browser at archaea.ucsc.edu.
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the ucsc Archaeal Genome browser
Nucleic Acids Research, 2006Co-Authors: Kevin L Schneider, Katherine S Pollard, Robert Baertsch, Andy Pohl, Todd M LoweAbstract:As more Archaeal Genomes are sequenced, effective research and analysis tools are needed to integrate the diverse information available for any given locus. The feature-rich UCSC Genome Browser, created originally to annotate the human Genome, can be applied to any sequenced organism. We have created a UCSC Archaeal Genome Browser, available at http://archaea.ucsc.edu/, currently with 26 Archaeal Genomes. It displays G/C content, gene and operon annotation from multiple sources, sequence motifs (promoters and Shine-Dalgarno), microarray data, multi-Genome alignments and protein conservation across phylogenetic and habitat categories. We encourage submission of new experimental and bioinformatic analysis from contributors. The purpose of this tool is to aid biological discovery and facilitate greater collaboration within the Archaeal research community.